text: This method is based on the single-strand conformation polymorphism analysis (SSCA) method developed for single-nucleotide polymorphism (SNP) analysis. SSCA differentiates between single-stranded DNA fragments of identical size but distinct sequence based on differential migration in non-denaturating electrophoresis.  In MS-SSCA, this is used to distinguish between bisulfite-treated, PCR-amplified regions containing the CpG sites of interest.  Although SSCA lacks sensitivity when only a single nucleotide difference is present, bisulfite treatment frequently makes a number of C-to-T conversions in most regions of interest, and the resulting sensitivity approaches 100%.  MS-SSCA also provides semi-quantitative analysis of the degree of DNA methylation based on the ratio of band intensities.  However, this method is designed to assess all CpG sites as a whole in the region of interest rather than individual methylation sites.